Ribosomes Kellie Halpenny Form and Function -Found on the rough endoplasmic reticulum or the cytoplasm -Also located within the mitochondria, and the chloroplast, but are only few in content -The ribosome is actually made up of two subunits, the small subunit and the large subunit, which only come together when converting mRNA information to amino acids. rRNA is the biggest part of ribosomes, being almost 60% of a ribosome’s weight. Because of the thousands of ribosomes each cell has, rRNA is the most abundant form of RNA in the human body. eukaryotic vs. prokaryotic In eukaryotic cells, three of the four ribosomal RNA strands are synthesized in the nucleolus, a structure in the nucleus. The fourth ribosomal RNA strand is synthesized outside of the nucleolus and then transported into the nucleolus for ribosome assembly. Prokaryotic cells lack a nucleus or nucleolus and therefor ribosomal synthesis takes place in the cytoplasms. function in protein synthesis -site of protein synthesis in the cytoplasm -used in translation - Translation is a process where genetic information is translated from a ``nucleic acid language" to an "amino acid language" using th genetic information encoded in a mRNA molecule, which is a type of ribonucleic acid that encodes genetic information from DNA and conveys it to the ribosomes. The ribosome assembles on the first start codon in the mRNA. Once the start codon is identified, each sequential group of three base pairs form the next codon. In this way the position of the start codon determines the open reading frame, or order of codons that will be read to form the protein. When a stop codon is encountered a termination factor (TF) binds to the mRNA and causes the ribosome to dissociate, releasing the protein. http://bioweb.uwlax.edu/GenWeb/Molecular/Theory/Translation/trans1.swf (This is a video of how translation works. You have to press the forward button a bunch) “small subunit RNA” as a tool for studying evolution Interlineage variation of ribosomal structure is used to establish a rigorous framework for considering the evolution of eubacterial, archaebacterial, and eukaryotic lineages. Key regions of the ribosome differ between bacteria and archaea, microbes that the researchers say are genetically closer to eukarya, the domain of life that includes humans. These "molecular signatures" were so pronounced that professor Carl Woese, who wrote a study of this at Illinois, concluded that the archaea comprised a separate domain of life, distinct from bacteria and eukarya (animals, plants, fungi and protists). He also found that ribosomal protein and RNA signatures, which they say is evidence that the ribosomal RNA and proteins co-evolved. Active Research
Harry Noller, MCD Biology Ribosomes are RNA-based molecular machines that are responsible for synthesis of proteins. Researchers in the Noller laboratory were the first to solve the complete structure of a ribosome using X-ray crystallography. Besides the importance of protein synthesis to understanding the molecular basis of cellular function, research on ribosomes promises to improve the design of new antibiotics. Many of today's most effective anti-microbial drugs work by targeting bacterial ribosomes. As pathogenic bacteria continue to develop resistance to commonly used antibiotics, clarification of the structure and molecular mechanisms of bacterial ribosomes will be critical for the design of new drugs that will keep pace with rapidly evolving bacteria.
Ribosome Research will Impact the Design of Antibiotics Besides the importance of protein synthesis to understanding the molecular basis of cellular function, research on ribosomes has paved the way to understanding how antibiotics work. Many of the most effective anti-microbial antibiotics, such as erythromycin, neomycin, spectinomycin, tylosin and tetracycline, work by targeting bacterial ribosomes, interfering with functions such as tRNA recognition, movement of tRNA through the ribosome (translocation), or joining the amino acids together (peptidyl transferase). However, in recent years, pathogenic bacteria have evolved a variety of mechanisms to become resistant to almost all of the commonly used antibiotics, which has led to a world-wide resurgence in serious illnesses caused by bacterial infections. An increased understanding of how the ribosome works, together with knowledge of its three-dimensional molecular structure, are now leading to strategies for the design of novel antibiotics
Function ·Ribosomes translate messenger RNA to synthesize proteins. ·They catalyze the assembly of individual amino acids into polypeptide chains, using an mRNA molecule as a template to join together the correct sequence of amino acids. ·The mRNA carries the coding information to the ribosomes. It tells the ribosomes what amino acids bond together and in what sequence. ·During protein synthesis various ribosomes line up along a single mRNA molecule and form a polysome. Structure ·Ribosomes are spherical and are found in all cells. ·They are composed of about 40% protein and 60% ribosomal RNA. ·They are composed of large and small subunits which join together when the ribosome attaches to the messenger RNA to synthesize protein. ·The large subunit contains the P and A sites, where transfer RNAs bind with the mRNA in protein synthesis. ·Eukaryote ribosomes are produced and assembled in the nucleolus. Three of the four strands are produced outside the nucleolus and transported inside to complete the ribosome assembly. The ribosomal proteins enter the nucleolus and combine with four strands to make the two subunits that will make up the complete ribosome. The ribosome units leave the nucleus through the nuclear pores and unite once in the cytoplasm. For prokaryotes, the ribosomes are made up of 3 strands and are produced in the cytoplasm. ·Ribosomes can also be found in chloroplasts and mitochondria of eukaryotes.
Free vs. bound ribosomes ·Free ribosomes are free to move in the cytosol and the protein formed in these ribosomes is used within the cytosol. ·The bound ribosomes are bound to the ER and the nuclear envelope and the protein from these ribosomes is used within the cell membrane. After the polypeptide chain is formed, it is extruded into the interior of the ER then it is transported to its destination. ·The presence of an ER Targeting Signal Sequence (a short polypeptide) on the protein being synthesized will determine if the ribosome is free or membrane bound.
Synthesizing a Protein ·First the small subunit binds to the mRNA and finds the start codon then the initiator tRNA binds to the mRNA. ·Then the large ribosome containing the P site and the A site binds to the small subunit. ·Next another tRNA carrying a different amino acid binds to the A site. ·The two amino acids form a peptide bond. ·The initiator tRNA is then released from the P site. ·The ribosome moves to the next codon and the tRNA in the A site shifts to the P site allowing the next tRNA to bind to the A site. ·The process continues and more amino acids bond together to form a polypeptide. ·When the ribosome reaches the stop codon there is not a tRNA attracted to it so the ribosome releases the polypeptide and splits into its subunits, which later reassemble to synthesize more proteins. Animation of protein synthesis: http://www.johnkyrk.com/DNAtranslation.html Recent Studies ·Yale University, “The Conformation of Ribosomes and rRNA” - In 2000 Professors Thomas Steitz and Peter Moore determined the atomic structure of the ribosome’s large subunit, paving the way for more effective drugs to fight infections. By knowing the structure of the large ribosomal subunit they can determine its exact structure with antibiotics bound to it. The information should enable pharmaceutical companies to devise new inhibitors of ribose function that can be used to control bacterial diseases that have become resistant to older antibiotics.
·University of California, “Translational Control in Biology and Medicine"- Professor Harry Noller has been studying ribosomes for over 30 years. Many of the most effective antibiotics work by targeting bacterial ribosomes and findings by Noller and others have led to the development of novel antibiotics for use against germs that have developeed resistance to current drugs, for example the drug-resistant staph infection. His team has also made an advancement in producing a high-resolution image of ribosomes that enables them to construct an atom-by-atom model of the ribosome.
·Colombia University, Professors Pallaiah Thammana and Charles R. Cantor, “Studies on Ribosomal Structure and Interactions near the m26Am26A Sequence.” - Antibodies raised against N6, N6- dimethyl adenosine were used to study the environment and role of the m26Am26A sequence in the E. coli ribosome. It is suggested that the m26Am26A sequence is located close to the initiator tRNA binding site of the 30s subunit during initiation of protein synthesis.
Bibliography
“Journey into the Cell: Ribosomes.” About.com. 2008. The New York Times Company. 17 Oct. 2008 <http://biology.about.com/library/weekly/aa033000a.htm>.
Kyrk, John. “RNA Translation.” Cartoon. RNA Translation. 21 Sept. 2008. 17 Oct. 2008 <http://www.johnkyrk.com/DNAtranslation.html>.
Marcey, David. “An Introduction to .” Callutheran Academic Programs. 2003. 17 Oct. 2008 <http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/ribosome/ribosome.htm>.
Peart, Karen. “Yale team solves atomic structure of ribosome unit .” Yale Bulletin and Calendar. 1 Sept. 2000. Yale University. 17 Oct. 2008 http://www.yale.edu/opa/arc-ybc/v29.n1/story3.html.
“Ribosome.” The Internet Encyclopedia of Science. 17 Oct. 2008 http://www.daviddarling.info/encyclopedia/R/ribosome.html.
“Ribosome.” Wikipedia. 22 Oct. 2008. Wikimedia Foundation, Inc. 17 Oct. 2008 http://en.wikipedia.org/wiki/Ribosome.
“Ribosomes.” CS Stewards . 17 Oct. 2008 http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Ribosomes/Ribosome.HTML.
“Ribosomes.” Kimball’s Biology Pages. 24 May 2006. 17 Oct. 2008 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/Ribosomes.html.
“Role of the Ribosome.” Cell Biology Graduate Program. 5 Dec. 2003. University of Texas Medical Branch. 17 Oct. 2008 <http://cellbio.utmb.edu/CELLBIO/ribosome.htm>.
Stephens, Tim. “New images reveal the workings of cellular protein factories.” UC Santa Cruz Currents Online. 2 Apr. 2001. 17 Oct. 2008 http://www.ucsc.edu/currents/00-01/04-02/ribosome.html
“Studies on ribosome structure and interactions near the m26A m26A sequence.” Nucleic Acids Research. 2008. Oxford Journal. 17 Oct. 2008 <http://nar.oxfordjournals.org/cgi/content/abstract/5/3/805?ck=nck>.
Kellie Halpenny
Form and Function
- Found on the rough endoplasmic reticulum or the cytoplasm
- Also located within the mitochondria, and the chloroplast, but are only few in content
- The ribosome is actually made up of two subunits, the small subunit and the large subunit, which only come together when converting mRNA information to amino acids. rRNA is the biggest part of ribosomes, being almost 60% of a ribosome’s weight. Because of the thousands of ribosomes each cell has, rRNA is the most abundant form of RNA in the human body.
eukaryotic vs. prokaryotic
In eukaryotic cells, three of the four ribosomal RNA strands are synthesized in the nucleolus, a structure in the nucleus. The fourth ribosomal RNA strand is synthesized outside of the nucleolus and then transported into the nucleolus for ribosome assembly.
Prokaryotic cells lack a nucleus or nucleolus and therefor ribosomal synthesis takes place in the cytoplasms.
function in protein synthesis
- site of protein synthesis in the cytoplasm
- used in translation
- Translation is a process where genetic information is translated from a ``nucleic acid language" to an "amino acid language" using th genetic information encoded in a mRNA molecule, which is a type of ribonucleic acid that encodes genetic information from DNA and conveys it to the ribosomes. The ribosome assembles on the first start codon in the mRNA. Once the start codon is identified, each sequential group of three base pairs form the next codon. In this way the position of the start codon determines the open reading frame, or order of codons that will be read to form the protein. When a stop codon is encountered a termination factor (TF) binds to the mRNA and causes the ribosome to dissociate, releasing the protein.
http://bioweb.uwlax.edu/GenWeb/Molecular/Theory/Translation/trans1.swf
(This is a video of how translation works. You have to press the forward button a bunch)
“small subunit RNA” as a tool for studying evolution
Interlineage variation of ribosomal structure is used to establish a rigorous framework for considering the evolution of eubacterial, archaebacterial, and eukaryotic lineages. Key regions of the ribosome differ between bacteria and archaea, microbes that the researchers say are genetically closer to eukarya, the domain of life that includes humans. These "molecular signatures" were so pronounced that professor Carl Woese, who wrote a study of this at Illinois, concluded that the archaea comprised a separate domain of life, distinct from bacteria and eukarya (animals, plants, fungi and protists). He also found that ribosomal protein and RNA signatures, which they say is evidence that the ribosomal RNA and proteins co-evolved.
Active Research
Harry Noller, MCD Biology
Ribosomes are RNA-based molecular machines that are responsible for synthesis of proteins. Researchers in the Noller laboratory were the first to solve the complete structure of a ribosome using X-ray crystallography. Besides the importance of protein synthesis to understanding the molecular basis of cellular function, research on ribosomes promises to improve the design of new antibiotics. Many of today's most effective anti-microbial drugs work by targeting bacterial ribosomes. As pathogenic bacteria continue to develop resistance to commonly used antibiotics, clarification of the structure and molecular mechanisms of bacterial ribosomes will be critical for the design of new drugs that will keep pace with rapidly evolving bacteria.
Ribosome Research will Impact the Design of Antibiotics
Besides the importance of protein synthesis to understanding the molecular basis of cellular function, research on ribosomes has paved the way to understanding how antibiotics work. Many of the most effective anti-microbial antibiotics, such as erythromycin, neomycin, spectinomycin, tylosin and tetracycline, work by targeting bacterial ribosomes, interfering with functions such as tRNA recognition, movement of tRNA through the ribosome (translocation), or joining the amino acids together (peptidyl transferase). However, in recent years, pathogenic bacteria have evolved a variety of mechanisms to become resistant to almost all of the commonly used antibiotics, which has led to a world-wide resurgence in serious illnesses caused by bacterial infections. An increased understanding of how the ribosome works, together with knowledge of its three-dimensional molecular structure, are now leading to strategies for the design of novel antibiotics
Bibliography
Alberts, Bruce. Molecular Biology of the Cell. New York: Garland Science, 2002.
Campbell, Neil A. Biology. 8th ed. San Francisco: Pearson Education, Inc., 2008.
Figure 12. Ribosomes and Polyribosomes - liver cell (TEM x173,400). Photograph.
Dennis Kunkel . Ed. M J Farabee. 2007. Estrella Mountain Community College.
19 Oct. 2008 <http://www.emc.maricopa.edu/faculty/farabee/BIOBK/
ribosome.gif>.
“Function of a Ribosome”. Wikipedia. 2008.
<http://wiki.answers.com/Q/What_is_the_function_of_a_ribosome>.
"Ribosomes." St. Edward's University Computer Science Web Site. 19 Oct. 2008
<http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Ribosomes/
Ribosome.HTML.>.
Ribosome translating a tRNA strand into a protein. Photograph.
RNA-Ribonucleic Acids. 19 Oct. 2008 <http://library.thinkquest.org/
04apr/00217/images/content/ribosome.jpg>.
“Roles of the Ribosome”.5 Dec. 2003. University Of Texas Medical Branch. 9 Oct. 2008 <http://cellbio.utmb.edu/cellbio/ribosome.htm>.
"Translation." BioWeb. Ed. Scott Cooper. 2006. University of Wisconsin System
Board of Regents. 19 Oct. 2008 <http://bioweb.uwlax.edu/GenWeb/Molecular/
Theory/Translation/translation.htm>.
Visionlearning. The Nucleotides of DNA. 2004.
<http://web.visionlearning.com/custom/biology/custum/BIO1.1-pg-dnanucleotides.shtml>.
Ribosome
Eivy Herrera-G
Function
· Ribosomes translate messenger RNA to synthesize proteins.
· They catalyze the assembly of individual amino acids into polypeptide chains, using an mRNA molecule as a template to join together the correct sequence of amino acids.
· The mRNA carries the coding information to the ribosomes. It tells the ribosomes what amino acids bond together and in what sequence.
· During protein synthesis various ribosomes line up along a single mRNA molecule and form a polysome.
Structure
· Ribosomes are spherical and are found in all cells.
· They are composed of about 40% protein and 60% ribosomal RNA.
· They are composed of large and small subunits which join together when the ribosome attaches to the messenger RNA to synthesize protein.
· The large subunit contains the P and A sites, where transfer RNAs bind with the mRNA in protein synthesis.
· Eukaryote ribosomes are produced and assembled in the nucleolus. Three of the four strands are produced outside the nucleolus and transported inside to complete the ribosome assembly. The ribosomal proteins enter the nucleolus and combine with four strands to make the two subunits that will make up the complete ribosome. The ribosome units leave the nucleus through the nuclear pores and unite once in the cytoplasm. For prokaryotes, the ribosomes are made up of 3 strands and are produced in the cytoplasm.
· Ribosomes can also be found in chloroplasts and mitochondria of eukaryotes.
Free vs. bound ribosomes
· Free ribosomes are free to move in the cytosol and the protein formed in these ribosomes is used within the cytosol.
· The bound ribosomes are bound to the ER and the nuclear envelope and the protein from these ribosomes is used within the cell membrane. After the polypeptide chain is formed, it is extruded into the interior of the ER then it is transported to its destination.
· The presence of an ER Targeting Signal Sequence (a short polypeptide) on the protein being synthesized will determine if the ribosome is free or membrane bound.
Synthesizing a Protein
· First the small subunit binds to the mRNA and finds the start codon then the initiator tRNA binds to the mRNA.
· Then the large ribosome containing the P site and the A site binds to the small subunit.
· Next another tRNA carrying a different amino acid binds to the A site.
· The two amino acids form a peptide bond.
· The initiator tRNA is then released from the P site.
· The ribosome moves to the next codon and the tRNA in the A site shifts to the P site allowing the next tRNA to bind to the A site.
· The process continues and more amino acids bond together to form a polypeptide.
· When the ribosome reaches the stop codon there is not a tRNA attracted to it so the ribosome releases the polypeptide and splits into its subunits, which later reassemble to synthesize more proteins.
Animation of protein synthesis: http://www.johnkyrk.com/DNAtranslation.html
Recent Studies
· Yale University, “The Conformation of Ribosomes and rRNA” - In 2000 Professors Thomas Steitz and Peter Moore determined the atomic structure of the ribosome’s large subunit, paving the way for more effective drugs to fight infections. By knowing the structure of the large ribosomal subunit they can determine its exact structure with antibiotics bound to it. The information should enable pharmaceutical companies to devise new inhibitors of ribose function that can be used to control bacterial diseases that have become resistant to older antibiotics.
· University of California, “Translational Control in Biology and Medicine"- Professor Harry Noller has been studying ribosomes for over 30 years. Many of the most effective antibiotics work by targeting bacterial ribosomes and findings by Noller and others have led to the development of novel antibiotics for use against germs that have developeed resistance to current drugs, for example the drug-resistant staph infection. His team has also made an advancement in producing a high-resolution image of ribosomes that enables them to construct an atom-by-atom model of the ribosome.
· Colombia University, Professors Pallaiah Thammana and Charles R. Cantor, “Studies on Ribosomal Structure and Interactions near the m26Am26A Sequence.” - Antibodies raised against N6, N6- dimethyl adenosine were used to study the environment and role of the m26Am26A sequence in the E. coli ribosome. It is suggested that the m26Am26A sequence is located close to the initiator tRNA binding site of the 30s subunit during initiation of protein synthesis.
Bibliography
“Journey into the Cell: Ribosomes.” About.com. 2008. The New York Times Company. 17 Oct. 2008 <http://biology.about.com/library/weekly/aa033000a.htm>.
Kyrk, John. “RNA Translation.” Cartoon. RNA Translation. 21 Sept. 2008. 17 Oct. 2008 <http://www.johnkyrk.com/DNAtranslation.html>.
Marcey, David. “An Introduction to .” Callutheran Academic Programs. 2003. 17 Oct. 2008 <http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/ribosome/ribosome.htm>.
Peart, Karen. “Yale team solves atomic structure of ribosome unit .” Yale Bulletin and Calendar. 1 Sept. 2000. Yale University. 17 Oct. 2008 http://www.yale.edu/opa/arc-ybc/v29.n1/story3.html.
“Ribosome.” The Internet Encyclopedia of Science. 17 Oct. 2008 http://www.daviddarling.info/encyclopedia/R/ribosome.html.
“Ribosome.” Wikipedia. 22 Oct. 2008. Wikimedia Foundation, Inc. 17 Oct. 2008 http://en.wikipedia.org/wiki/Ribosome.
“Ribosomes.” CS Stewards . 17 Oct. 2008 http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Ribosomes/Ribosome.HTML.
“Ribosomes.” Kimball’s Biology Pages. 24 May 2006. 17 Oct. 2008 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/Ribosomes.html.
“Role of the Ribosome.” Cell Biology Graduate Program. 5 Dec. 2003. University of Texas Medical Branch. 17 Oct. 2008 <http://cellbio.utmb.edu/CELLBIO/ribosome.htm>.
Stephens, Tim. “New images reveal the workings of cellular protein factories.” UC Santa Cruz Currents Online. 2 Apr. 2001. 17 Oct. 2008 http://www.ucsc.edu/currents/00-01/04-02/ribosome.html
“Studies on ribosome structure and interactions near the m26A m26A sequence.” Nucleic Acids Research. 2008. Oxford Journal. 17 Oct. 2008 <http://nar.oxfordjournals.org/cgi/content/abstract/5/3/805?ck=nck>.